X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GMH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG3350 or PEG8000, ammonium sulfate, sodium citrate pH 5.0, Tris-HCl pH 7.5, NaCl
Crystal Properties
Matthews coefficientSolvent content
2.6854.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.754α = 90
b = 138.504β = 90
c = 148.462γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2016-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.7750.011000.99427.41352528
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.772.860.959

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5GMH2.7750.0149888255099.90.21390.2120.2518RANDOM34.391
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.82-0.461.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.768
r_dihedral_angle_4_deg19.128
r_dihedral_angle_3_deg16.504
r_dihedral_angle_1_deg7.122
r_angle_refined_deg1.684
r_angle_other_deg1.102
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.768
r_dihedral_angle_4_deg19.128
r_dihedral_angle_3_deg16.504
r_dihedral_angle_1_deg7.122
r_angle_refined_deg1.684
r_angle_other_deg1.102
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12470
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing